Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2mhja1 CCCCEEEEEEEEECCCCCCHHHHHHHHCCCCC---------CEEC-----HHHHHHHHHHHHHHHHHCCCCCCEEECCCCCCCC----EEEEEEEECC------- >P1;d2qdfa1 -CCCEECCEEEEECCCCCCHHHHHHCCCCCC---------CCEEC-----HHHHHHHHHHHHCC----CCEE-EE-EEEEEC------CEEEEEEEEC------- >P1;d2qdfa2 ----CEEEEEEEECCCCCCHHHHHHHHH------CCCCCCCCCCC-----CCCHHHHHHHHHHHHHHHCCCCCEE-EEEEEEEC-CCEEEEEEEEECCCC----- >P1;d4xgab1 ----CEEEEEEEECCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCC-----HHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCEEEEEEEEECCCC----- >P1;d4xgab2 ----CEEEEEEEEEECCCCHHHHHCCCC---------CCCCCCCC-----HHHHHHHHHHHHHHHHCCCCCCCEE-EEEEEEECCCCEEEEEEEEECCCCCC--- >P1;d6j09a1 -C-CEECCCCCCCCCCCHHHHHHHHHCCCCC---------CCEEC-----HHHHHHHHHHHHHC----CCEE-EE-EEEEEC------CEEEEEEEEC------- >P1;d6j09a2 ----CEEEEEEEECCCCCCHHHHHHHHH------HCCCCCCCCCC-----HHHHHHHHHHHHHHHHHCCCCCCEE-EEEEEEEC-CCEEEEEEEEECC-C----- >P1;d6j09a3 ----C-CCEEEEECCCCCCHHHHCCCCCCCCC-------CCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCCCCCCCEEEEEEECCCC----- >P1;d6j09a4 ----CEEEEEEEEECCCCCHHHHHHHCC------C--CCCCEECC-----HHHHHHHHHHHHHHHHHCCCCCCEE-EEECCEECCCCEEEEEEEEECCCCCCCCC PSA >P1;d2mhja1 8585140670504a08528395036207512a---------9604-----35506500530051037494990405033b905a----1304040617------- >P1;d2qdfa1 -a94150640606619518696049303085---------95604-----a8316403730482----6305-30-60556b------6101030605------- >P1;d2qdfa2 ----140250504809408695057303------96b16475807-----5942881268024204646077060-70525737-892030404080696----- >P1;d4xgab1 ----2406404064093283940154060228319759a453525-----893176017403510474819906056163743987821402030716a6----- >P1;d4xgab2 ----3605506065711b16a5057307---------18982735-----5761671145037004744148070-6072556796620306040408975b--- >P1;d6j09a1 -a-315068050421a991387048703086---------75504-----99314502651485----9407-40-60847b------7101050615------- >P1;d6j09a2 ----140360607706416494038305------856056b2805-----5850660085048602858586060-71407639-8a30403040618-7----- >P1;d6j09a3 ----1-04506068175177930372071529-------670735a9966285077015303530496516909067163732a86670602010807b6----- >P1;d6j09a4 ----4404405056925b0575065216------a--07496725-----5830371174048303845175070-70537547996210010404078565a8b Translating the sequences *****EEEEEEEECCCCCCHHHHHH**C****---------C**C-----HHHHHHHHHHHHHHHH*CCCCCCEE********C----EEEEEEEECC------- -****E**EEEEECCCCCCHHHHHH*CC***---------CC**C-----HHHHHHHHHHHH**----CC**-EE-EEEEE*------*EEEEEEE*C------- ----CEEEEEEEECCCCCCHHHHHH***------*****CCC*CC-----***HHHHHHHHHHHHH**CCCCCEE-EEEEE**C-CC*EEEEEEEECC*C----- ----CEEEEEEEECCCCCCHHHHH**CC***********CCC*CC-----HHHHHHHHHHHHHHHH*CCCCCCEE*EEEEE**C*CC*EEEEEEEECC*C----- ----CEEEEEEEE**CCCCHHHHH**CC---------**CCC*CC-----HHHHHHHHHHHHHHHH*CCCCCCEE-EEEEE**C*CC*EEEEEEEECC*C**--- -*-**E*******CCCC**HHHHHH*CC***---------CC**C-----HHHHHHHHHHHHH*----CC**-EE-EEEEE*------*EEEEEEE*C------- ----CEEEEEEEECCCCCCHHHHHH***------*****CCC*CC-----HHHHHHHHHHHHHHHH*CCCCCCEE-EEEEE**C-CC*EEEEEEEECC-C----- ----C-**EEEEECCCCCCHHHH***CC****-------CCC*CC*******HHHHHHHHHHHHHH*CCCCCCEE*EEEEE**C*CC**EEEEEEECC*C----- ----CEEEEEEEE*CCCCCHHHHHH*CC------*--**CC**CC-----HHHHHHHHHHHHHHHH*CCCCCCEE-EEE****C*CC*EEEEEEEECC*C***** 310598.tem _________________________________ ----CEEEEEEEECCCCCCHHHHHH*CC***---*--**CCC*CC-----HHHHHHHHHHHHHHHH*CCCCCCEE-EEEEE**C*CC*EEEEEEEECC*C----- Structural block scores 0 3 - 4.3 M 6.5 24.6 75.0 75.0 75.0 40.9 75.0 75.0 75.0 5 12 E 4.5 M 3.2 3.4 2.5 3.0 3.5 3.5 3.2 12.0 2.8 13 18 C 4.8 H 5.6 5.0 4.8 4.3 4.4 5.4 4.0 4.8 5.6 19 24 H 4.8 H 4.3 5.7 5.3 3.7 5.6 5.0 4.7 4.8 4.7 26 27 C 4.2 M 3.5 1.5 1.5 3.0 3.5 1.5 2.5 3.5 3.5 28 30 * 3.2 M 2.7 4.3 75.0 1.3 75.0 4.7 75.0 2.7 75.0 31 33 - 4.5 M 53.5 75.0 75.0 4.0 75.0 75.0 75.0 53.0 75.0 35 36 - 4.0 M 75.0 75.0 8.8 6.0 75.0 75.0 5.5 75.0 75.0 37 38 * 3.2 M 75.0 75.0 3.5 9.8 4.5 75.0 2.5 75.0 3.5 39 41 C 4.6 H 53.0 29.7 5.3 4.0 6.3 29.0 6.5 4.3 6.3 43 44 C 4.5 M 2.0 2.0 3.5 3.5 4.0 2.0 2.5 4.0 3.5 45 49 - 4.7 H 75.0 75.0 75.0 75.0 75.0 75.0 75.0 8.1 75.0 50 65 H 4.8 H 2.6 13.1 4.1 3.7 3.6 13.2 3.9 3.3 3.6 67 72 C 4.6 H 5.8 27.3 4.0 5.2 3.5 28.3 5.3 4.5 3.7 73 74 E 5.0 H 2.0 1.5 3.0 3.0 3.5 2.0 3.0 4.5 3.5 76 80 E 4.6 H 5.3 4.4 3.8 4.6 4.0 5.0 3.8 4.8 4.4 81 82 * 1.6 P 2.5 43.2 5.0 3.5 5.5 43.2 4.5 2.5 4.5 85 86 C 4.4 M 75.0 75.0 8.5 7.5 6.0 75.0 9.2 6.0 7.5 88 95 E 4.9 H 2.2 2.1 2.4 2.1 2.1 2.5 2.1 2.1 1.2 96 97 C 4.7 H 4.0 2.5 3.0 3.5 4.0 3.0 4.5 3.5 3.5 100 104 - 4.6 H 75.0 75.0 75.0 75.0 48.3 75.0 75.0 75.0 8.2 >>>>>>